The overall goal of this proposal is the development of a three-dimensional optical tomographic (OT) near-infrared imaging system for oximetry in small animals. The system will be designed to allow for co-registration of OT data and magnetic resonance (MR) imaging data, but may also be used as a stand-alone optical imaging unit. While commercial systems that perform optical blood-oxygenation monitoring exist, these instruments have not been optimized for small animal studies and have not been combined with MR imaging systems. Furthermore, the available devices often operate with a limited number of sources and detectors, do not generate three-dimensional volumetric images, and the image reconstruction is performed with diffusion-theory-based algorithms. It is well known, however, that diffusion theory does not fully account for the effects of light propagation in small biological media (diameter 1-2 cm), because at these dimensions the diffusion approximation to the more generally applicable theory of radiative transfer is not sufficiently accurate. The proposed work attempts to overcome the current shortfalls and develop a near-infrared optical imaging system that can be used in combination with standard small animal MR scanners. The main hypothesis of this project is that current limitations of optical tomographic imaging can be addressed by implementing a three-dimensional frequency-domain reconstruction scheme that is based on the equation of radiative transfer (ERT). This algorithm will be implemented and used in conjunction with a commercially available frequency-domain measurement system (IAMGENT from ISS, Urban-Champaign, IL), which will be adapted to collect data inside an MR small animal imager. By co-registering optical and MR data one can combine the benefits of MR's high-spatial-resolution, with OT's high temporal resolution and its capability of separating oxyhemoglobin, deoxyhemoglobin, and blood volume effects. For this project we will pursue the following three specific aims: (1) Develop and numerically validate of a three-dimensional, transport-theory-based, frequency-domain image reconstruction code for diffuse optical tomography; (2) Validate and evaluate the optical tomographic imaging system (code and instrument) in a small animal magnetic resonance imager; and (3) Compare frequency-domain and steady-state, transport-theory based optical tomography with diffusion-theory-based optical tomography. This comparison will quantify the advantages and disadvantages of these different optical imaging modalities.